# Re: [Freesurfer] Multiple comparison using Monte Carlo

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Dear Dr. Douglas,```
```
Thank you so much for your detailed response.

The simulation here is to get the probability of a maximum cluster that
size or larger in the cached CSD files. It checks the probability of  the
cluster size but have nothing to do with the analysis metrics that I have
used. Do I understand correctly?

Best regards,
Ting Li

On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

>
>
> On 12/2/2019 11:58 AM, Ting Li wrote:
>
>         External Email - Use Caution
> Dear Dr. Douglas,
>
> Thank you so much for your quick response! You saved my half life.
>
> From the introduction of clusterwise correction for multiple comparisons,
> I have a few questions.
>
> 1, What is the null hypothesis here ?
>
> In the tutorial, the null hypothesis is that there is no effect of age
> (age slope = 0)
>
> 2, What is a z map? Do you mean synthesize cortical datasets?
>
> A z-map is just a map where all the values are from a gaussian
> distribution with mean=0 and stddev=1. This just assigns a random z-value
> to each vertex on fsaverage
>
> 3. Smooth z map, what FWHM do you use, if it is not consistent with my
> FWHM, how will it affect the results?
>
> The FWHM comes from an estimate from the residuals of the analysis. The
> residuals are everything that does not fit the linear model and represent
> noise. We use the residuals to estimate the underlying smoothness (FWHM),
>
> 4, Threshold z map, what does level mean? Does it mean the vertex p-value?
>
> Basically, it is the vertex p-value, but we use  the "sig" = -log10(p).
> You also have to specify the sign. If you have an a priori hypothesis about
> the direction, then you can specify pos (positive) or neg (negative). If
> you do not have an a priori hypothesis, then use abs (for absolute, for an
> unsigned test).
>
>
> Clusterwise Correction for Multiple Comparisons
> To perform a cluster-wise correction for multiple comparisons, we will run
> a simulation. The simulation is a way to get a measure of the distribution
> of the maximum cluster size under the *null **hypothesis*. This is done
> by iterating over the following steps:
> 1. Synthesize a z map
> 2. Smooth z map (using residual FWHM)
> 3. Threshold z map (level and sign)
> 4. Find clusters in thresholded map
> 5. Record area of maximum cluster
> 6. Repeat over desired number of iterations (usually > 5000)
>
> Thank you so much!
>
> Best regards,
> Ting
>
> On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. <
> dgr...@mgh.harvard.edu> wrote:
>
>> That will use the pre-computed ("cached") CSD files distributed with
>> FreeSurfer. This used 10,000 iterations.
>>
>> On 12/1/2019 11:34 PM, Ting Li wrote:
>>
>>         External Email - Use Caution
>> Dear Freesurfer Expert:
>>
>> I have used the simulation code as show below:
>>
>> mri_glmfit-sim \
>>   --glmdir lh.gender_age.glmdir \
>>   --cache 4 neg \
>>   --cwp  0.05\
>>   --2spaces
>>
>> My question is how many iterations are done during this simulation? I
>> didn’t specify the iteration number.
>>
>> Why I didn’t have the csd file?
>>
>> Thanks a lot for your response!
>>
>> Best regards,
>> Ting
>>
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